Genome Sequencing of a Severe Acute Respiratory Syndrome Coronavirus 2 Isolate Obtained from a South African Patient with Coronavirus Disease 2019

Mushal Allam; Arshad Ismail; Zamantungwa T H Khumalo; Stanford Kwenda; Peter van Heusden; Ruben Cloete; Constantinos Kurt Wibmer; Phillip Senzo Mtshali; Florah Mnyameni; Thabo Mohale; Kathleen Subramoney; Sibongile Walaza; Wendy Ngubane; Nevashan Govender; Nkengafac V Motaze; Jinal N Bhiman; SA-COVID-19 response team

doi:10.1128/MRA.00572-20

Genome Sequencing of a Severe Acute Respiratory Syndrome Coronavirus 2 Isolate Obtained from a South African Patient with Coronavirus Disease 2019

Microbiol Resour Announc. 2020 Jul 2;9(27):e00572-20. doi: 10.1128/MRA.00572-20.

Authors

Mushal Allam¹, Arshad Ismail², Zamantungwa T H Khumalo², Stanford Kwenda², Peter van Heusden³, Ruben Cloete³, Constantinos Kurt Wibmer², Phillip Senzo Mtshali², Florah Mnyameni², Thabo Mohale², Kathleen Subramoney², Sibongile Walaza^{2

4}, Wendy Ngubane², Nevashan Govender², Nkengafac V Motaze^{2

5}, Jinal N Bhiman; SA-COVID-19 response team

Affiliations

¹ National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa mushala@nicd.ac.za.
² National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.
³ South African Medical Research Council Bioinformatics Capacity Development Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
⁴ School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
⁵ Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.

Abstract

As a contribution to the global efforts to track and trace the ongoing coronavirus pandemic, here we present the sequence, phylogenetic analysis, and modeling of nonsynonymous mutations for a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome that was detected in a South African patient with coronavirus disease 2019 (COVID-19).